I was not aware the MRQ used the layers function this way as I work primarily on the gameplay side. I’ll have to do a bit of research on the topic for now.
There is no way to convert a world partition world into a world composition world once it’s been translated. However, you could select everything in the world outliner, copy, ctrl+n to create a new level, choose the empty one, then paste everything back in. This is not optimal but since the converter only goes one way this is the current workaround.